Genetic diversity and population structure analysis of goat breeds of Pakistan

Goats are among the earliest domesticated livestock species, known for their adaptability to diverse climates. Pakistan, with thirty-five indigenous goat breeds and the world’s third-largest goat population, requires genomic characterization to support effective conservation and selection programs. In this study, the data for 827 individuals representing seven Punjab breeds (Beetal, Barbari, Daira Din Panah, Nachi, Pahari, Pothwari, and Teddi) genotyped using the GoatSNP50 Illumina chip were retrieved. After stringent quality control (call rate ≥90%, MAF ≥5%, HWE P<0.0001), 38,890 autosomal SNPs were retained for further analysis. Genetic diversity and relationships among breeds were investigated using principal component analysis (PCA) and linkage disequilibrium (LD) decay profiles with PLINK v1.9.0 and PopLDdecay, respectively. Population structure was evaluated with ADMIXTURE v1.3.0 (K=2–7), selecting the model with the lowest cross-validation error. Allele-based breed-specific markers were identified using a pipeline already established by our group to support breed conservation programs. PCA revealed discrete clustering of breeds based on genetic structure, with Teddi being most distinct breed. Other breeds, including Barbari, Beetal, Daira Din Panah, Nachi, Pahari, and Pothwari, showed partial overlap but remained generally distinguishable. LD decay analysis (using SNP correlation, r², over 100 kb) indicated that Barbari, Daira Din Panah, and Nachi were more uniform as they maintained higher LD at longer distances; however, Teddi and Beetal exhibited faster LD decay, reflecting greater genetic diversity. ADMIXTURE analysis revealed the higher allelic sharing and extensive crossbreeding among breeds, precluding the identification of any breed-specific markers. In conclusion, this study demonstrates genetic stratification and diversity among goat breeds from the Punjab region of Pakistan, but exhibits considerable allelic sharing and gene flow, likely due to crossbreeding. Future studies should target pure-bred animals with higher-density SNP panels or whole-genome resequencing for better understanding of population structure and to validate breed-specific markers.